I made the same mistake one time, changing the Crusade target from Egypto Jerusalem, only to realize the Duchy of Palestine was in Egypt. It was... embarrassing. This is why you make sure to check de jures and swap Crusade targets just in case.
I personally don't think this in particular is a reason to have de jure drift have a game rule (the AI is weighted to pick targets by the weighting duchies are given. If Palestine de jure drifts to Egypt and jerusalem is left with just one duchy (I assume Outer Jordan also drifted somewhere), then the weighting should shift to Egypt, too, since it now has the Holy Site and high-weight duchies (or at least one high weight duchy), plus it's closer.
However, I do think it is, in general, just a good feature to have a de jure drift rule, to crank up or down the drift speed or even just completely remove it to preserve the initial balance of realms.